Interpretive Summary: For chicken and other agricultural species, there is growing interest and reliance on the ability to assay large numbers of genetic markers. Of particular interest are genetic markers known as single nucleotide polymorphisms or SNPs as they are highly abundant and can be typed using high throughput platforms. In this paper, we describe the development of a chicken “chip” that can query 60,000 (60K) SNPs. This resource has been widely distributed to the poultry community, which has enhanced the ability of researchers to identify genes of agricultural importance, improve the chicken genetic map and genome assembly, and be applied in genomic selection. The end result is greatly increased knowledge and power to improve poultry breeding.

Technical Abstract:
In livestock species like the chicken, high throughput SNP genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). We describe the design of a moderate density (60K) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at medium to high minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines, using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x, and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total, we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable, and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two microchrocmosomes not covered by the current genome assembly.